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| cyclic_loess | Cyclic Loess normalization for Hi-C data |
| exportJuicebox | Export multiHiCcompare results for visualization in Juicebox |
| fastlo | Perform fast loess normalization on a Hi-C experiment |
| HCT116_r1 | A 4 column sparse matrix for a Hi-C matrix. |
| HCT116_r2 | A 4 column sparse matrix for a Hi-C matrix. |
| HCT116_r3 | A 4 column sparse matrix for a Hi-C matrix. |
| HCT116_r4 | A 4 column sparse matrix for a Hi-C matrix. |
| HCT116_r5 | A 4 column sparse matrix for a Hi-C matrix. |
| HCT116_r6 | A 4 column sparse matrix for a Hi-C matrix. |
| hg19_cyto | A GenomicRanges object containing centromeric, gvar, and stalk regions. |
| hg38_cyto | A GenomicRanges object containing centromeric, gvar, and stalk regions. |
| Hicexp-class | An S4 class for working with Hi-C data |
| hicexp2 | hicexp object with 4 samples from two groups. |
| hicexp_diff | hicexp object with 7 samples from two groups. |
| hic_exactTest | Perform exact test based difference detection on a Hi-C experiment |
| hic_filter | Perform filtering on a Hi-C experiment |
| hic_glm | Function to perform GLM differential analysis on Hi-C experiment |
| hic_scale | Perform library scaling on a hicexp object |
| hic_table | Print the hic_table |
| hic_table-method | Print the hic_table |
| make_hicexp | Make Hi-C experiment object from data |
| manhattan_hicexp | Manhattan plot function for results of multiHiCcompare |
| MD_composite | Plot a composite MD plot with the results of a comparison |
| MD_hicexp | Make MD plots for all combinations of a condition |
| meta | Print the metadata |
| meta-method | Print the metadata |
| normalized | Print the indicator for if the data is normalized |
| normalized-method | Print the indicator for if the data is normalized |
| perm_test | Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompare |
| plot_counts | Plot the count results from topDirs |
| plot_pvals | Plot the p-value results from topDirs |
| pval_heatmap | Function to visualize p-values from multiHiCcompare results |
| resolution | Print the resolution |
| resolution-method | Print the resolution |
| results | Print the results |
| results-method | Print the results |
| show-method | Print information about a HiCexp object |
| smartApply | Function to apply either biocParallel or standard lapply |
| topDirs | Filter results of multiHiCcompare |